9IIT

Full length structure of FKP in complex with GTP and GDP

Summary for 9IIT

• Entry DOI: 10.2210/pdb9iit/pdb
• Related: 9iip 9iis
• Descriptor: L-fucokinase/L-fucose-1-P guanylyltransferase, GUANOSINE-5'-TRIPHOSPHATE, FORMIC ACID, ... (8 entities in total)
• Functional Keywords: fucose, atp, gtp, kinase, pyrophosphorylase, transferase
• Biological source: Bacteroides fragilis
• Total number of polymer chains: 2
• Total formula weight: 218603.64

Authors

Ko, T.P.,Lin, S.W.,Hsu, M.F.,Lin, C.H. (deposition date: 2024-06-21, release date: 2025-03-05, Last modification date: 2025-04-09)

Primary citation

Lin, S.W.,Ko, T.P.,Chiang, H.Y.,Wu, C.G.,Hsu, M.F.,Wang, A.H.,Lin, C.H.
Structural insight into the catalytic mechanism of the bifunctional enzyme l-fucokinase/GDP-fucose pyrophosphorylase.
J.Biol.Chem., 301:108344-108344, 2025

PubMed Abstract: The bifunctional L-fucokinase/GDP-β-L-fucose pyrophosphorylase (FKP) from Bacteroides fragilis catalyzes the conversion from L-fucose to GDP-β-L-fucose. The reaction product, representing the activated form of L-fucose, is used by all L-fucosyltransferases to incorporate L-fucose. Herein we report the first X-ray crystal structures of FKP in complex with substrate/product, leading to the dissection of both activity domains and corresponding catalytic mechanisms. The full length (FKP-FL, 949 amino acids) exists as a tetramer in solution, but the individually prepared N-terminal domain (FKP-NTD corresponding to the sequence 1-496, also containing a SUMO tag) and C-terminal (FKP-CTD, the sequence 519-949) form a monomer and a dimer, respectively. FKP-NTD has a single α/β domain and a β-helix-containing domain, whereas FKP-CTD folds into two α/β domains and the linker comprises three α-helices. The β-L-fucose-1-phosphate (fucose-1-P) and GTP bound separately to the active sites of fucokinase (located at FKP-CTD) and pyrophosphorylase (FKP-NTD), and a third nucleotide binding site is adjacent to the β-helix (also in FKP-NTD). Furthermore, Asp762 was proposed to serve as the general base in the reaction of fucokinase, to deprotonate the C1-OH of fucose in the nucleophilic attack to γ-phosphate of ATP, resulting in the formation of fucose-1-P. At the same time, Arg592 and magnesium ion stabilize the developing negative charge in the leaving group (ADP). Subsequently, in the pyrophosphorylase-catalyzed reaction, the Lys187 side chain facilitates the nucleophilic attack of fucose-1-P toward GTP, leading to the formation of GDP-fucose.

PubMed: 39993526
DOI: 10.1016/j.jbc.2025.108344

Experimental method

X-RAY DIFFRACTION (2.3 Å)